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Ancient DNA sequences point to a large loss of mitochondrial genetic diversity in the saiga antelope (Saiga tatarica) since the Pleistocene.

https://arctichealth.org/en/permalink/ahliterature100381
Source
Mol Ecol. 2010 Nov;19(22):4863-75
Publication Type
Article
Date
Nov-2010
Author
Paula F Campos
Tommy Kristensen
Ludovic Orlando
Andrei Sher
Marina V Kholodova
Anders Götherström
Michael Hofreiter
Dorothée G Drucker
Pavel Kosintsev
Alexei Tikhonov
Gennady F Baryshnikov
Eske Willerslev
M Thomas P Gilbert
Author Affiliation
Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen, Denmark.
Source
Mol Ecol. 2010 Nov;19(22):4863-75
Date
Nov-2010
Language
English
Publication Type
Article
Abstract
Prior to the Holocene, the range of the saiga antelope (Saiga tatarica) spanned from France to the Northwest Territories of Canada. Although its distribution subsequently contracted to the steppes of Central Asia, historical records indicate that it remained extremely abundant until the end of the Soviet Union, after which its populations were reduced by over 95%. We have analysed the mitochondrial control region sequence variation of 27 ancient and 38 modern specimens, to assay how the species' genetic diversity has changed since the Pleistocene. Phylogenetic analyses reveal the existence of two well-supported, and clearly distinct, clades of saiga. The first, spanning a time range from >49,500 (14) C ybp to the present, comprises all the modern specimens and ancient samples from the Northern Urals, Middle Urals and Northeast Yakutia. The second clade is exclusive to the Northern Urals and includes samples dating from between 40,400 to 10,250 (14) C ybp. Current genetic diversity is much lower than that present during the Pleistocene, an observation that data modelling using serial coalescent indicates cannot be explained by genetic drift in a population of constant size. Approximate Bayesian Computation analyses show the observed data is more compatible with a drastic population size reduction (c. 66-77%) following either a demographic bottleneck in the course of the Holocene or late Pleistocene, or a geographic fragmentation (followed by local extinction of one subpopulation) at the Holocene/Pleistocene transition.
PubMed ID
20874761 View in PubMed
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A biochemical--biophysical study of hemoglobins from woolly mammoth, Asian elephant, and humans.

https://arctichealth.org/en/permalink/ahliterature132571
Source
Biochemistry. 2011 Aug 30;50(34):7350-60
Publication Type
Article
Date
Aug-30-2011
Author
Yue Yuan
Tong-Jian Shen
Priyamvada Gupta
Nancy T Ho
Virgil Simplaceanu
Tsuey Chyi S Tam
Michael Hofreiter
Alan Cooper
Kevin L Campbell
Chien Ho
Author Affiliation
Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States.
Source
Biochemistry. 2011 Aug 30;50(34):7350-60
Date
Aug-30-2011
Language
English
Publication Type
Article
Keywords
Alkanesulfonic Acids - chemistry
Amino Acid Sequence
Animals
Biophysical Processes
Blood Substitutes - metabolism
Buffers
Elephants
Hemoglobin A2 - chemistry - metabolism
Hemoglobins - chemistry - metabolism
Humans
Hydrogen-Ion Concentration
Mammoths
Molecular Sequence Data
Morpholines - chemistry
Oxygen - metabolism
Phosphates - chemistry
Temperature
Abstract
This study is aimed at investigating the molecular basis of environmental adaptation of woolly mammoth hemoglobin (Hb) to the harsh thermal conditions of the Pleistocene ice ages. To this end, we have carried out a comparative biochemical-biophysical characterization of the structural and functional properties of recombinant hemoglobins (rHb) from woolly mammoth (rHb WM) and Asian elephant (rHb AE) in relation to human hemoglobins Hb A and Hb A(2) (a minor component of human blood). We have obtained oxygen equilibrium curves and calculated O(2) affinities, Bohr effects, and the apparent heat of oxygenation (?H) in the presence and absence of allosteric effectors [inorganic phosphate and inositol hexaphosphate (IHP)]. Here, we show that the four Hbs exhibit distinct structural properties and respond differently to allosteric effectors. In addition, the apparent heat of oxygenation (?H) for rHb WM is less negative than that of rHb AE, especially in phosphate buffer and the presence of IHP, suggesting that the oxygen affinity of mammoth blood was also less sensitive to temperature change. Finally, (1)H NMR spectroscopy data indicates that both a(1)(ß/d)(1) and a(1)(ß/d)(2) interfaces in rHb WM and rHb AE are perturbed, whereas only the a(1)d(1) interface in Hb A(2) is perturbed compared to that in Hb A. The distinct structural and functional features of rHb WM presumably facilitated woolly mammoth survival in the Arctic environment.
Notes
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PubMed ID
21806075 View in PubMed
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Climate impacts on transocean dispersal and habitat in gray whales from the Pleistocene to 2100.

https://arctichealth.org/en/permalink/ahliterature261021
Source
Mol Ecol. 2015 Apr;24(7):1510-22
Publication Type
Article
Date
Apr-2015
Author
S Elizabeth Alter
Matthias Meyer
Klaas Post
Paul Czechowski
Peter Gravlund
Cork Gaines
Howard C Rosenbaum
Kristin Kaschner
Samuel T Turvey
Johannes van der Plicht
Beth Shapiro
Michael Hofreiter
Source
Mol Ecol. 2015 Apr;24(7):1510-22
Date
Apr-2015
Language
English
Publication Type
Article
Abstract
Arctic animals face dramatic habitat alteration due to ongoing climate change. Understanding how such species have responded to past glacial cycles can help us forecast their response to today's changing climate. Gray whales are among those marine species likely to be strongly affected by Arctic climate change, but a thorough analysis of past climate impacts on this species has been complicated by lack of information about an extinct population in the Atlantic. While little is known about the history of Atlantic gray whales or their relationship to the extant Pacific population, the extirpation of the Atlantic population during historical times has been attributed to whaling. We used a combination of ancient and modern DNA, radiocarbon dating and predictive habitat modelling to better understand the distribution of gray whales during the Pleistocene and Holocene. Our results reveal that dispersal between the Pacific and Atlantic was climate dependent and occurred both during the Pleistocene prior to the last glacial period and the early Holocene immediately following the opening of the Bering Strait. Genetic diversity in the Atlantic declined over an extended interval that predates the period of intensive commercial whaling, indicating this decline may have been precipitated by Holocene climate or other ecological causes. These first genetic data for Atlantic gray whales, particularly when combined with predictive habitat models for the year 2100, suggest that two recent sightings of gray whales in the Atlantic may represent the beginning of the expansion of this species' habitat beyond its currently realized range.
PubMed ID
25753251 View in PubMed
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Emergence of a chimeric globin pseudogene and increased hemoglobin oxygen affinity underlie the evolution of aquatic specializations in Sirenia.

https://arctichealth.org/en/permalink/ahliterature298533
Source
Mol Biol Evol. 2019 Mar 04; :
Publication Type
Journal Article
Date
Mar-04-2019
Author
Anthony V Signore
Johanna L A Paijmans
Michael Hofreiter
Angela Fago
Roy E Weber
Mark S Springer
Kevin L Campbell
Author Affiliation
Department of Biological Sciences, University of Manitoba, Winnipeg, Canada.
Source
Mol Biol Evol. 2019 Mar 04; :
Date
Mar-04-2019
Language
English
Publication Type
Journal Article
Abstract
As limits on O2 availability during submergence impose severe constraints on aerobic respiration, the oxygen binding globin proteins of marine mammals are expected to have evolved under strong evolutionary pressures during their land-to-sea transition. Here we address this question for the order Sirenia by retrieving, annotating, and performing detailed selection analyses on the globin repertoire of the extinct Steller's sea cow (Hydrodamalis gigas), dugong (Dugong dugon), and Florida manatee (Trichechus manatus latirostris) in relation to their closest living terrestrial relatives (elephants and hyraxes). These analyses indicate most loci experienced elevated nucleotide substitution rates during their transition to a fully aquatic lifestyle. While most of these genes evolved under neutrality or strong purifying selection, the rate of non-synonymous/synonymous replacements increased in two genes (Hbz-T1 and Hba-T1) that encode the a-type chains of hemoglobin (Hb) during each stage of life. Notably, the relaxed evolution of Hba-T1 is temporally coupled with the emergence of a chimeric pseudogene (Hba-T2/Hbq-ps) that contributed to the tandemly linked Hba-T1 of stem sirenians via interparalog gene conversion. Functional tests on recombinant Hb proteins from extant and ancestral sirenians further revealed that the molecular remodeling of Hba-T1 coincided with increased Hb-O2 affinity in early sirenians. Available evidence suggests this trait evolved to maximize O2 extraction from finite lung stores and suppress tissue O2 offloading, thereby facilitating the low metabolic intensities of extant sirenians. By contrast, the derived reduction in Hb-O2 affinity in (sub)Arctic Steller's sea cows is consistent with fueling increased thermogenesis by these once colossal marine herbivores.
PubMed ID
30828717 View in PubMed
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Influence of climate warming on arctic mammals? New insights from ancient DNA studies of the collared lemming Dicrostonyx torquatus.

https://arctichealth.org/en/permalink/ahliterature96767
Source
PLoS One. 2010;5(5):e10447
Publication Type
Article
Date
2010
Author
Stefan Prost
Nickolay Smirnov
Vadim B Fedorov
Robert S Sommer
Mathias Stiller
Doris Nagel
Michael Knapp
Michael Hofreiter
Author Affiliation
Research Group Molecular Ecology, Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany. stefan.prost@gmi.oeaw.ac.at
Source
PLoS One. 2010;5(5):e10447
Date
2010
Language
English
Publication Type
Article
Abstract
BACKGROUND: Global temperature increased by approximately half a degree (Celsius) within the last 150 years. Even this moderate warming had major impacts on Earth's ecological and biological systems, especially in the Arctic where the magnitude of abiotic changes even exceeds those in temperate and tropical biomes. Therefore, understanding the biological consequences of climate change on high latitudes is of critical importance for future conservation of the species living in this habitat. The past 25,000 years can be used as a model for such changes, as they were marked by prominent climatic changes that influenced geographical distribution, demographic history and pattern of genetic variation of many extant species. We sequenced ancient and modern DNA of the collared lemming (Dicrostonyx torquatus), which is a key species of the arctic biota, from a single site (Pymva Shor, Northern Pre Urals, Russia) to see if climate warming events after the Last Glacial Maximum had detectable effects on the genetic variation of this arctic rodent species, which is strongly associated with a cold and dry climate. RESULTS: Using three dimensional network reconstructions we found a dramatic decline in genetic diversity following the LGM. Model-based approaches such as Approximate Bayesian Computation and Markov Chain Monte Carlo based Bayesian inference show that there is evidence for a population decline in the collared lemming following the LGM, with the population size dropping to a minimum during the Greenland Interstadial 1 (B?lling/Aller?d) warming phase at 14.5 kyrs BP. CONCLUSION: Our results show that previous climate warming events had a strong influence on genetic diversity and population size of collared lemmings. Due to its already severely compromised genetic diversity a similar population reduction as a result of the predicted future climate change could completely abolish the remaining genetic diversity in this population. Local population extinctions of collared lemmings would have severe effects on the arctic ecosystem, as collared lemmings are a key species in the trophic interactions and ecosystem processes in the Arctic.
PubMed ID
20523724 View in PubMed
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Million-year-old DNA sheds light on the genomic history of mammoths.

https://arctichealth.org/en/permalink/ahliterature311364
Source
Nature. 2021 03; 591(7849):265-269
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Date
03-2021
Author
Tom van der Valk
Patrícia Pecnerová
David Díez-Del-Molino
Anders Bergström
Jonas Oppenheimer
Stefanie Hartmann
Georgios Xenikoudakis
Jessica A Thomas
Marianne Dehasque
Ekin Saglican
Fatma Rabia Fidan
Ian Barnes
Shanlin Liu
Mehmet Somel
Peter D Heintzman
Pavel Nikolskiy
Beth Shapiro
Pontus Skoglund
Michael Hofreiter
Adrian M Lister
Anders Götherström
Love Dalén
Author Affiliation
Centre for Palaeogenetics, Stockholm, Sweden. tom.vandervalk@scilifelab.se.
Source
Nature. 2021 03; 591(7849):265-269
Date
03-2021
Language
English
Publication Type
Journal Article
Research Support, Non-U.S. Gov't
Keywords
Acclimatization - genetics
Alleles
Animals
Bayes Theorem
DNA, Ancient - analysis - isolation & purification
Elephants - genetics
Europe
Evolution, Molecular
Female
Fossils
Genetic Variation - genetics
Genome, Mitochondrial - genetics
Genomics
Mammoths - genetics
Markov Chains
Molar
North America
Phylogeny
Radiometric Dating
Siberia
Time Factors
Abstract
Temporal genomic data hold great potential for studying evolutionary processes such as speciation. However, sampling across speciation events would, in many cases, require genomic time series that stretch well back into the Early Pleistocene subepoch. Although theoretical models suggest that DNA should survive on this timescale1, the oldest genomic data recovered so far are from a horse specimen dated to 780-560 thousand years ago2. Here we report the recovery of genome-wide data from three mammoth specimens dating to the Early and Middle Pleistocene subepochs, two of which are more than one million years old. We find that two distinct mammoth lineages were present in eastern Siberia during the Early Pleistocene. One of these lineages gave rise to the woolly mammoth and the other represents a previously unrecognized lineage that was ancestral to the first mammoths to colonize North America. Our analyses reveal that the Columbian mammoth of North America traces its ancestry to a Middle Pleistocene hybridization between these two lineages, with roughly equal admixture proportions. Finally, we show that the majority of protein-coding changes associated with cold adaptation in woolly mammoths were already present one million years ago. These findings highlight the potential of deep-time palaeogenomics to expand our understanding of speciation and long-term adaptive evolution.
PubMed ID
33597750 View in PubMed
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Origin and history of mitochondrial DNA lineages in domestic horses.

https://arctichealth.org/en/permalink/ahliterature99769
Source
PLoS One. 2010;5(12):e15311
Publication Type
Article
Date
2010
Author
Michael Cieslak
Melanie Pruvost
Norbert Benecke
Michael Hofreiter
Arturo Morales
Monika Reissmann
Arne Ludwig
Author Affiliation
Leibniz Institute for Zoo and Wildlife Research, Evolutionary Genetics, Berlin, Germany.
Source
PLoS One. 2010;5(12):e15311
Date
2010
Language
English
Publication Type
Article
Abstract
Domestic horses represent a genetic paradox: although they have the greatest number of maternal lineages (mtDNA) of all domestic species, their paternal lineages are extremely homogeneous on the Y-chromosome. In order to address their huge mtDNA variation and the origin and history of maternal lineages in domestic horses, we analyzed 1961 partial d-loop sequences from 207 ancient remains and 1754 modern horses. The sample set ranged from Alaska and North East Siberia to the Iberian Peninsula and from the Late Pleistocene to modern times. We found a panmictic Late Pleistocene horse population ranging from Alaska to the Pyrenees. Later, during the Early Holocene and the Copper Age, more or less separated sub-populations are indicated for the Eurasian steppe region and Iberia. Our data suggest multiple domestications and introgressions of females especially during the Iron Age. Although all Eurasian regions contributed to the genetic pedigree of modern breeds, most haplotypes had their roots in Eastern Europe and Siberia. We found 87 ancient haplotypes (Pleistocene to Mediaeval Times); 56 of these haplotypes were also observed in domestic horses, although thus far only 39 haplotypes have been confirmed to survive in modern breeds. Thus, at least seventeen haplotypes of early domestic horses have become extinct during the last 5,500 years. It is concluded that the large diversity of mtDNA lineages is not a product of animal breeding but, in fact, represents ancestral variability.
PubMed ID
21187961 View in PubMed
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Prehistoric genomes reveal the genetic foundation and cost of horse domestication.

https://arctichealth.org/en/permalink/ahliterature262115
Source
Proc Natl Acad Sci U S A. 2014 Dec 30;111(52):E5661-9
Publication Type
Article
Date
Dec-30-2014
Author
Mikkel Schubert
Hákon Jónsson
Dan Chang
Clio Der Sarkissian
Luca Ermini
Aurélien Ginolhac
Anders Albrechtsen
Isabelle Dupanloup
Adrien Foucal
Bent Petersen
Matteo Fumagalli
Maanasa Raghavan
Andaine Seguin-Orlando
Thorfinn S Korneliussen
Amhed M V Velazquez
Jesper Stenderup
Cindi A Hoover
Carl-Johan Rubin
Ahmed H Alfarhan
Saleh A Alquraishi
Khaled A S Al-Rasheid
David E MacHugh
Ted Kalbfleisch
James N MacLeod
Edward M Rubin
Thomas Sicheritz-Ponten
Leif Andersson
Michael Hofreiter
Tomas Marques-Bonet
M Thomas P Gilbert
Rasmus Nielsen
Laurent Excoffier
Eske Willerslev
Beth Shapiro
Ludovic Orlando
Source
Proc Natl Acad Sci U S A. 2014 Dec 30;111(52):E5661-9
Date
Dec-30-2014
Language
English
Publication Type
Article
Keywords
Animals
Animals, Domestic - genetics
Cardiovascular System - anatomy & histology
Dogs
Evolution, Molecular
Genome - physiology
Hindlimb - anatomy & histology - physiology
Horses - anatomy & histology - genetics
Humans
Inbreeding
Russia
Abstract
The domestication of the horse ~ 5.5 kya and the emergence of mounted riding, chariotry, and cavalry dramatically transformed human civilization. However, the genetics underlying horse domestication are difficult to reconstruct, given the near extinction of wild horses. We therefore sequenced two ancient horse genomes from Taymyr, Russia (at 7.4- and 24.3-fold coverage), both predating the earliest archeological evidence of domestication. We compared these genomes with genomes of domesticated horses and the wild Przewalski's horse and found genetic structure within Eurasia in the Late Pleistocene, with the ancient population contributing significantly to the genetic variation of domesticated breeds. We furthermore identified a conservative set of 125 potential domestication targets using four complementary scans for genes that have undergone positive selection. One group of genes is involved in muscular and limb development, articular junctions, and the cardiac system, and may represent physiological adaptations to human utilization. A second group consists of genes with cognitive functions, including social behavior, learning capabilities, fear response, and agreeableness, which may have been key for taming horses. We also found that domestication is associated with inbreeding and an excess of deleterious mutations. This genetic load is in line with the "cost of domestication" hypothesis also reported for rice, tomatoes, and dogs, and it is generally attributed to the relaxation of purifying selection resulting from the strong demographic bottlenecks accompanying domestication. Our work demonstrates the power of ancient genomes to reconstruct the complex genetic changes that transformed wild animals into their domesticated forms, and the population context in which this process took place.
Notes
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PubMed ID
25512547 View in PubMed
Less detail

Species-specific responses of Late Quaternary megafauna to climate and humans.

https://arctichealth.org/en/permalink/ahliterature129951
Source
Nature. 2011 Nov 17;479(7373):359-64
Publication Type
Article
Date
Nov-17-2011
Author
Eline D Lorenzen
David Nogués-Bravo
Ludovic Orlando
Jaco Weinstock
Jonas Binladen
Katharine A Marske
Andrew Ugan
Michael K Borregaard
M Thomas P Gilbert
Rasmus Nielsen
Simon Y W Ho
Ted Goebel
Kelly E Graf
David Byers
Jesper T Stenderup
Morten Rasmussen
Paula F Campos
Jennifer A Leonard
Klaus-Peter Koepfli
Duane Froese
Grant Zazula
Thomas W Stafford
Kim Aaris-Sørensen
Persaram Batra
Alan M Haywood
Joy S Singarayer
Paul J Valdes
Gennady Boeskorov
James A Burns
Sergey P Davydov
James Haile
Dennis L Jenkins
Pavel Kosintsev
Tatyana Kuznetsova
Xulong Lai
Larry D Martin
H Gregory McDonald
Dick Mol
Morten Meldgaard
Kasper Munch
Elisabeth Stephan
Mikhail Sablin
Robert S Sommer
Taras Sipko
Eric Scott
Marc A Suchard
Alexei Tikhonov
Rane Willerslev
Robert K Wayne
Alan Cooper
Michael Hofreiter
Andrei Sher
Beth Shapiro
Carsten Rahbek
Eske Willerslev
Author Affiliation
Centre for GeoGenetics, University of Copenhagen, Øster Voldgade 5-7, DK-1350 Copenhagen K, Denmark.
Source
Nature. 2011 Nov 17;479(7373):359-64
Date
Nov-17-2011
Language
English
Publication Type
Article
Keywords
Animals
Bayes Theorem
Biota
Bison
Climate Change - history
DNA, Mitochondrial - analysis - genetics
Europe
Extinction, Biological
Fossils
Genetic Variation
Geography
History, Ancient
Horses
Human Activities - history
Humans
Mammals - genetics - physiology
Mammoths
Molecular Sequence Data
Population Dynamics
Reindeer
Siberia
Species Specificity
Time Factors
Abstract
Despite decades of research, the roles of climate and humans in driving the dramatic extinctions of large-bodied mammals during the Late Quaternary period remain contentious. Here we use ancient DNA, species distribution models and the human fossil record to elucidate how climate and humans shaped the demographic history of woolly rhinoceros, woolly mammoth, wild horse, reindeer, bison and musk ox. We show that climate has been a major driver of population change over the past 50,000 years. However, each species responds differently to the effects of climatic shifts, habitat redistribution and human encroachment. Although climate change alone can explain the extinction of some species, such as Eurasian musk ox and woolly rhinoceros, a combination of climatic and anthropogenic effects appears to be responsible for the extinction of others, including Eurasian steppe bison and wild horse. We find no genetic signature or any distinctive range dynamics distinguishing extinct from surviving species, emphasizing the challenges associated with predicting future responses of extant mammals to climate and human-mediated habitat change.
Notes
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PubMed ID
22048313 View in PubMed
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